We are pioneering the development of 'modular rational design' and novel 'in vitro selection' protocols that offer new and powerful approaches for the creation of highly specific allosteric RNA and DNA enzymes. We will use both rational and combinatorial strategies to create new catalytic nucleic acids whose rates can be specifically controlled by small organic compounds, proteins, nucleic acids or any other physical signal. These design strategies already have proven to be highly effective for the creation of allosteric RNA enzymes and are expected to produce similar results with new RNA enzymes and DNA enzymes. We envision a series of possible allosteric ribozyme mechanisms and we will create and characterize examples of each class. Through this process, we intend to provide a solid conceptual and experimental framework for interactions between distinct RNA structural domains and for the engineering of new nucleic acid enzymes. In addition, we will test the function of these 'molecular switches' in vivo, to establish a new method of controlled gene expression.